Mystery of the Matrix
by JenniferRSong
Summary: Matrix Prime: Where you can live out your fantasies in the safety of the virtual world. When the Doctor, Amy, and Rory visit, they find themselves in a fight to separate fantasy from reality. But at what cost? Rory/Amy. *NOW COMPLETE*
1. Chapter 1

So, my very first, multichapter, 11th Doctor story. It took me a full 2 seasons to try my hand at this. Here's hoping I've gotten the hang of this Doctor's personality. If not, I'm sure I'll be chastised in the reviews.

I'm aiming for a chapter a day until the end of the year, 11 chapters total, with a bonus section to be posted on New Year's Day. Please enjoy and leave reviews to let me know this didn't go to waste. I spent something like 6 months pulling it together so that I could post a completed story.

_Edit: 1-5-12. Added disclaimer, which I can't believe I forgot in the first place. Minor punctuation changes._

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Plot Summary: On Matrix Prime, people can hook themselves up to machines and live out their fantasies. But it comes with a cost: the life energy of the people. They live out their fantasies, which may take place over years, but in reality, their bodies wither away quickly.

When Amy, Rory, and the Doctor visit, they are tricked into hooking into the Matrix. Now it is a race to separate fantasy from reality and a fight to free the Doctor, if Amy and Rory can free themselves first.

Takes place after "Let's Kill Hitler" but anytime before "The Girl Who Waited."

References: The Matrix, Surrogates, Repo Men, Batman Forever, Star Trek: Generations

Doctor Who: Amy's Choice, the Rebel Flesh/Gangers

**DISCLAIMER: **I do not own Doctor Who, which includes any and all references made to people/places/items owned by the BBC. I own all OC chars and species presented for this story.

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Preface

Three figures were walking on a ramp, one at a brisk pace, the other two a little slower as they gazed around in wonderment. Rows upon rows, stacks upon stacks of people lying in tilted tubes, sleeping. Monitors beside each tube showed their vital signs and how long they had been there.

"Won't this be wonderful?" said one, a woman, gushing. "It's been twenty-five years since our honeymoon and we'll be back on that lost planet, literally like it was yesterday."

"That's nice, honey," said the other, a man, her husband apparently. He was a little disconcerted at the sleeping people, clad only in a simple white gown.

"Oh, for heaven's sake, Harvey, you could be a little happier!" she snipped. "This is a once in a lifetime opportunity! It was lucky I found this place!"

He shrank back a little. "Sorry, Flo. I just don't have a very good feeling is all."

They arrived at two empty tubes. The figure that had led them there, a small humanoid creature about three feet tall and a sort of orangey color, held out a webbed hand for Flo to grasp as she climbed in, her dark hair carefully tucked behind her head. Beside her, Harvey clambered in without assistance, shaking his head. To their temples, the creature stuck disks with wires trailing from it.

"Not a good feeling at all."

With a hiss, the tubes slid shut. A gas began to fill the tubes as the couple relaxed. Within seconds, they were breathing at a slow, even pace.

The creature looked up. Above, hidden in an alcove, a figure nodded. The creature began to turn dials and press buttons.

In the tubes, strands of Flo's hair began to turn white.

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_(Amy Pond voiceover)_

_When I was a little girl, I had an imaginary friend, and when I grew up, he came back. _

_He's called the Doctor, he comes from somewhere else, he's got a box called the TARDIS that's bigger on the inside and can travel anywhere in time and space. _

_I ran away with him and we've been running ever since._

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MATT SMITH

KAREN GILLIAN

ARTHUR DARVILL

DOCTOR WHO

MYSTERY OF THE MATRIX

by

Jennifer R. Song

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Chapter 1

_THWACK!_

_DING!  
><em>

_HISS!_

"OW!"

It was to a myriad of loud sounds that the Ponds walked into. At the moment, the Doctor was trying to drive the TARDIS with his left hand and was sucking on two fingers on his right. When he noticed Amy and Rory, he swiftly yanked his fingers out and wiped them on his pants.

"Oh, morning!"

"Mornin' Doctor," said Amy. "What did you do the TARDIS to make her burn you?"

"Oh, I thought she needed some recalibrating, she thought she didn't, and let me know so."

Another hiss from the console seemed to be the old ship's way of both confirming and warning him not to do it again. The Doctor tried to glare at the console, but his concentration was broken by the column suddenly stopping.

"We've landed," stated Rory, now used telling the difference between being in flight and being solid.

"Any idea where?" asked Amy.

The Doctor pulled the computer screen around and pressed a button. "Matrix Prime. 32nd century, roughly. This place is known for its in-depth virtual reality. Perfect way to have a holiday _without_ risking your life."

Amy rolled her eyes. "Boring."

"I dunno, what if you wanted to skydive?" asked Rory. "I mean, I wouldn't, you know, in reality. But virtual? You don't get hurt, you can't die, but you get the whole adrenalin thrill."

The Doctor pointed triumphantly at Rory. "See? He's got it. Let's go!"

With a bound, he was out the door.

"I swear, for someone that's hundreds of years older, he's about as eager as a kid in a candy store," muttered Amy.

"Not arguing."

The Doctor stuck his head back in. "Come along, Ponds. We've exploring to do."

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They had parked in a small closet, which, when they emerged, found themselves in a large, completely white waiting room. It was completely silent, except for a single humanoid in the middle of the room. Its orange skin and matching hair stood out from behind the transparent computer screen it was situated behind. Rory's shoes squeaked as they approached…him? Her? It? The creature looked up.

"Name." The voice was, more or less, feminine.

"Oh, hello, I'm the Doctor, this is Amy and Rory–"

"Appointment?"

"Ah, no, we're just dropping by, you know, thought it'd make a nice vacation."

She looked at him through the screen. Blinked. Then pressed a button on the desk. The buzz echoed loudly off the walls.

A door appeared from nowhere on the white wall. Three of the orange creatures came out, dressed in some kind of white uniform.

"You will go with them."

"If this is your idea of security, not much," said Amy as one grabbed her by her right hand and yanked her along.

"Um, Amy, I don't think they're security," said Rory as another grasped his left hand and pulled him after her.

"No, they're not," concurred the Doctor, sidestepping the last one and quickly striding to catch up to his companions.

They were led up a winding path. Sometimes, doors would open from the walls, allowing them to see more of the creatures at work as they came and went. Some were computer rooms, projecting unintelligible data. Others were repair rooms, where they could see long, slender tubes being disassembled or reassembled. A few had experiments going in, if the smoke and bubbling from what looked like Buson burners were any indication.

Finally, they reached a frosted pair of doors, unique in that while the other doors had been invisible until activated, this pair clearly was meant to draw attention.

"Oh, goody, whoever is in charge," said the Doctor, grinning.

The doors slid open.

"Ah, welcome, welcome."

A middle-aged man, slightly balding, came running up to them. He pumped their hands excitedly.

"We were beginning to think you wouldn't show up."

"We're expected?" asked Amy.

"Well, of course," said the man. "Oh, how rude of me, my name is Benedict. Benedict Cummings. And you are?"

"I'm the Doctor, she's Amy, he's Rory." The Doctor spread his hands out. "Here as requested."

Benedict nodded his head, breathless. "Yes, I've requested that they send diagnosticians again and again. But they keep saying they can't spare a soul. Well, looks like they managed three, eh?"

He clapped the Doctor on the back.

"Let's get you three down to the testing room, shall we?"

Amy and Rory had enough time to send each other a look of uncertainty before the little creatures poked them into following Benedict.

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The room was quiet, save for the soft hum of machinery. A dozen mostly gutted tube devices were linked into a wall, computers plugged into them flashing red and green lights. Two of the creatures, wearing lab coats, were studying the results.

"We've been having a bit of an issue with some of the VR-pods. There's some kind of, almost virus, in the system."

"Almost virus?" queried the Doctor.

"Well, most of the time it registers on the system as a valid program, which was actually put in, I checked with the manufacturer. And then sometimes, it pops up as a high-threat virus and demands that some programs be deleted for the safety of the system."

"How are you still running the place, then?" said Amy.

"Oh, it's only a small percentage of VR-pods that are affected, about 5% at the most." He gestured at the row. "This is one set of about, oh, near 50 affected."

The Doctor took out the sonic screwdriver and began scanning the devices. One of the orange humanoids squealed in horror.

"No, no, no, it's ok, see, just scanning."

It relaxed, seeing as the device had not interfered with their work.

Rory spoke up. "Um, Mr. Cummings? What are these guys called?"

"Benedict, please. And they are called Zharytes."

Amy snorted. "Look like Oomaph-loopas to me."

"Amy," said the Doctor warningly.

"Sorry. They just do."

"Unfortunately, their home planet was destroyed in a freak supernova a few centuries ago. The only ones left are here on Matrix Prime."

The Doctor kept silent as he continued to scan. Another race, another world lost because of him and the Time Lords and the Time War.

His contemplation ceased as he realized the only way to actually deal with this problem.

"We're going in."

"Sorry, what, it just sounded like you said we're going in," said Amy. Her time spent in the birthing chamber had caused her to be a bit more claustrophobic than usual. "If there's a computer problem, the last place we wanna be is inside, right?"

"Wrong, 'cause if there's a problem in there, we can find the problem and fix it from the inside." He turned to Benedict.

"Time to plug in."

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"Okay, there will be some slight discomfort as your system adjusts," said Benedict, hooking up Rory to one of half a dozen, definitely put back together, VR-pods. Amy was fidgeting with a temple pad. It itched. And that not-so-nice stomach lurching wasn't helping either. "You'll just need to relax, and let your mind float free. Oh, and you might experience some, ah, other issues we haven't yet been able to sort out."

"Ready, Ponds?"

"Nope."

"Nu-uh"

The Doctor grinned. "Neither am I."

A brilliant light.

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There's the set up. So what do you think their fantasies will be?


	2. Chapter 2

It's funny, I thought this chapter was longer than 3 pages in word. Oh well. Thanks to the one reviewer thus far. This chapter, find out their fantasies.

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Chapter 2

When he came to, Rory was surprised to find himself back in the TARDIS.

"Ergh."

Benedict was only a bit right; it was more than "slight discomfort". He felt nauseated and couldn't figure out why. He decided to remain on his back for the moment.

"Hit your head again?"

He started. "Amy?"

She was leaning over him, an eyebrow raised. "Yeah, that's my name."

He pressed his hands to his forehead. "Why is everything spinning?"

"Yeah, you hit your head," she said, rolling her eyes. "That's kinda what happens when you do, everything gets a little blurry. Just rest, you'll be back to working on the TARDIS in no time."

She left the console room.

And then it sank in what she said.

"Working on the…only the Doctor works on the TARDIS."

Finally, he got to his feet and chanced a look in a mirror device he remembered being on the console. He bit his tongue to keep from screaming.

The Doctor's face was reflected back at him.

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"Amelia? Amelia? Ameeelia!"

"I'm fine, Doctor, really. Stop shouting."

Amy sat up, feeling like a herd of elephants was tap dancing in her head. At least her stomach was settling down. Beside her, the Doctor gazed at her worryingly.

"I thought maybe we passed a little too close to that cosmic storm," he said, offering a cup of water. She took it gratefully. She looked around. Everything still looked the same.

"I'm ok, Doctor, I really am," she reassured him.

"All right, Amelia."

"Why do you keep calling me that?

"What?"

"Amelia. You know I prefer Amy."

He had a look of utter confusion on his face. "Since when?"

"Since I was a teenager."

He chuckled. "I think I'd know if sometime during your teenage years you'd decided to change to Amy."

A rock sank into her gut.

"Doctor, how long have I been travelling with you?"

Now he really was confused. "You really don't remember?

She shrugged.

"Amelia, I promised you I'd only be five minutes and I was. You've been travelling with me since you were seven years old."

Once, that would have been the most joyful words she could ever hear. Now, as she looked at her ringless finger, she wondered how that ever could have occurred to her.

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"Do you mind? That light is really bright."

There was someone shining a light in first one eye, then another. Once his vision cleared, he got a good view of who had been doing that.

He blinked. Closed his eyes, shook his head. Opened his eyes again.

"Master?"

The man in question tilted his head. "Really, Theta?"

"Doctor," he corrected. "I haven't been called Theta in centuries."

The Master snorted. "Where have I been, then? Hmm?"

And he walked off, muttering to himself. The Doctor sat up and looked around. He was in a highly advanced medical bay, from the look of things. Overhead, a full body scan was showing perfectly fine vitals. He sat up, groaning.

"Now then," said the Master, causing him to jump. "I wish you'd listen to me more. I _told_ you not to wear the heavy robe, but no, Mr. 'I'm Lord President, if I want to wear the fancy one I will.' And what happens? You tripped and hit your head. You're lucky that didn't cause another regeneration. Once was plenty enough, you said."

The Doctor stared at the Master, who continued to ramble on. It then occurred to him that this was the same face he'd last seen the Master wearing, just before his own regeneration. It also occurred to him that the Master was wearing orange Time Lord formal robes and holding a similar set in his arms, though this one had swirls of Gallifreyan writing listing very important titles.

"What?" snapped the Master. "Am I not supposed to show concern or something?" He held out the robes. "Now this is the lighter set I recommended you wear in the first place. _So wear them_."

And with a pointed look, he was out the door. A second later, he poked his head back in.

"And no trying to figure out how to add a bowtie to it!"

"Bowties are cool," the Doctor muttered, pulling the light-weight robe over the white shift-like under-robe he was wearing. He tried to push his hair under the hat, but the flop was determined to stick out from underneath, causing it to balance awkwardly on his head. A glance in the mirror had him sticking his tongue out at his reflection as he waltzed out.

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So, did you guess right? Or did I throw a timey-wimey ball at you?


	3. Chapter 3

About the same size as the last chapter. Hmm. I can assure you the chapters will get longer and more interesting.

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Chapter 3

Rory panicked. He closed his eyes and swallowed hard. He opened his eyes again. Yeah, still the same reflection.

He looked down. He was dressed in the Doctor's outfit, tweed and bowtie and all. Otherwise, he still looked like he had his own body.

That nauseated feeling was still there. Plus, his chest felt like he was having a ping-pong tournament in it.

Right, he decided, first things first. He needed to find out if there was anything he needed to know medically about the Doctor.

As if by habit, he took out the sonic screwdriver and gave himself a quick scan. With a start, he realized he understood what the device was saying.

Two hearts? Well, that certainly would explain the ping-pong feeling. He closed his eyes and listened.

_Thump-thump-thump-thump. Left-Right-Left-Right._

It was almost hypnotic, a quick 1-2-3-4 double heartbeat.

Otherwise, his biology seemed unchanged. Well, except for that presence in the back of his head. It was like someone was sharing his mind, but not completely. Realization hit him. That was the TARDIS he felt in the head. There was the translation bit, of course, but this was a different sensation. It was like singing, but he couldn't understand it.

"Better then?"

He gave a start as Amy popped back in, wearing a two-piece swimsuit and a towel around her waist. In his chest, both hearts seemed to leap in excitement. It felt _really_ weird.

"Yeah, all good. Where to next?"

She grinned, gesturing at herself. "Well, I am dressed for Rio."

Ah, good, she'd asked for one he'd seen the Doctor program in. Grateful for that, he began pulling levers and flipping switches. With a final throw, the central column began to move up and down.

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Two hours after that, they were both collapsed inside the TARDIS, out of breath.

"Well, at least it was Rio," said Rory helpfully.

"Yeah, well, you were a couple of million years off," muttered Amy, pulling leaves and twigs out of her hair. At least she had changed into regular clothes before they set off into the pre-historical forest.

Rory sighed, hurt by the insinuation that it was his fault the TARDIS had thought Rio circa 75 million BC would be more enjoyable than lounging on a beach. Was this how the Doctor felt every time he tried to get them somewhere, but ended up in a completely different environment?

If so, he hated to think what the old ship would think of next.

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Amy stared at the Doctor, her eyes wide. He stared right back, green eyes puzzled. She swallowed.

"You're serious," he stated.

"Where's Rory?" she rebutted.

Again, the blank stare. "Rory who?"

"Rory, my husband – well, he was my husband – he _is _my husband – oh, this is very confusing."

He helped her up. "Shall I do a search on him?"

She rubbed her forehead. "Please."

"Name? Probably lots of Rorys in the universe."

"Rory Williams, um, born in Leadworth like me, same time."

There was a clickity-clack of the old typewriter cum computer. A ding.

"Here we go. Rory Williams."

He swung the screen around to her. Her eyes drank in her husband's face, glad to know he existed here.

"Says here he died when he was 17."

Her heart froze. "Died?"

"Car accident. Swerved to avoid something in the road and hit a tree."

She gently touched his face on the screen. A tear slid down her cheek.

This was as bad as the Dream Lord's world. Except here, she hadn't even gotten the chance to say goodbye.

And without Rory, that meant she never had Melody.

She turned and ran into the belly of the TARDIS.

At the console, the Doctor's reflection in the screen twisted as the image cut out.

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The twin suns shone on the face as he drank in the sights of bustling Time Lords and glistening towers. For a moment, he just stood there, staring. Then…

"Lord President!"

A smile broke across his face. "Romana!"

She had regenerated again, he noted as he welcomed her with open arms. She laughed as he realized that hugging her was different in this incarnation than his fourth. For one thing, they were roughly the same height. And secondly, his hat chose that moment to pitch forward and he had to let go of her to catch it.

"Whoops, sorry there."

"Honestly, have you tried pins? They work wonders."

He _hmmed_. "I'll have to try that."

The two walked off, one a figment, the other wishing it was more than that.

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In the room the three were in, a switch was flipped. The tubes began to glow.

Inside their tubes, the hair on Amy and Rory's temples began to turn white. In the Doctor's tube, the tip of his hair flop turned white.

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So, one thing I am curious about, who would play Romana in a new incarnation? I've read stories with Kate Beckinsale in the role. What other British actress would you like to see in her role?


	4. Chapter 4

This chapter actually focuses more on Rory's POV, with a little Amy and Doctor. It's a bit longer than the previous ones. Please enjoy!

Oh, and not sure if the hints in this chapter warrant a T-rating. I'll stick with K+ for now, unless I'm advised differently.

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Chapter 4

It was late at night, TARDIS time. Amy was sleeping in her room. After exploring for a few hours without feeling tired, Rory found himself in what he could only assume was the Doctor's room. The bedcovers were covered in strange writing that he found he partially understood. On the walls were integrated bookshelves. The books were labeled with more of the strange symbols as titles. He scanned the shelves, hoping to find an interesting one.

He found one, sitting all by itself on a shelf, with not a speck of dust upon it. The cover bore two Greek letters that he recognized: Theta Sigma.

Taking off the tweed jacket and throwing it aside, he settled into a comfy chair and tilted the bendy light downwards. He cracked the old book open.

The first page had the symbols again, and below that, the words "My Life" written in the swirly language. He turned the page again. The next page bore a symbol which gradually resolved into the number "One." The following pictures were in black and white, and rather old. An old man stood with a young woman, probably a teenage. She had elfin features and was wearing a school girl's uniform. He was dressed in a Victorian manner, with a cane in his hands. His white hair was combed neatly back. Below the picture was written: "Myself and my granddaughter Susan."

Rory felt a bit guilty. Here he was, looking through the Doctor's things without permission. Then, a twinge of sadness. The Doctor had had a granddaughter, which meant he must have had a family back on his home planet, a planet that was now gone, by the Doctor's own hand.

He turned the page. The two were standing there, but with another pair of people. It was captioned "Ian and Barbara."

There were more pictures, of more companions, with different versions of the Doctor. A short Doctor ("Two") that looked like a hobo stood next to a young man wearing a kilt (Jamie McCrimmon) and a young woman in a sparkly jumpsuit (Zoe). Another Doctor ("Three"), with curly white hair, wearing velvet and lace, standing with a professional woman (Liz Shaw), then a more lost looking one (Jo Grant). Brigadier Alistair Gordon Lethbridge-Stewart stood with John Benton, Mike Yates and a bunch of others clad in military uniform. Funny, he never thought the Doctor would willingly work with military people.

"Four" was tall, with an impossibly long scarf, brown curls everywhere (like River's blond hair, he thought) and a toothy smile. Sarah Jane Smith (there were a lot of pictures of her, some with tear drops staining them). Harry Sullivan. Leela (Rory quickly paged through _those_ pictures). Romana I, which had only one and Romana II, who had a few. Rory realized that he must be looking at another Time Lord or Lady, whatever the women called themselves. In some pictures was a metal robot labeled K-9.

"Five" was dressed in a cricket outfit and looking almost as young as his Doctor. Pictures following were Nyssa of Traken and Tegan Jovancha. A separate picture was marked Adric. Written underneath was "I'm sorry." There was what looked like gold fragments stuck to the page and Rory gingerly turned the page, lest they come unstuck. A red-headed man, pale and worn, was next: Vislor Turlough.

"Six" made Rory's eyes hurt just looking at him. He was quite glad for the bowtie now. Peri Brown in a swimsuit nearly made him drop the book, but he recovered and quickly turned the page. Melanie Bush was next.

For a thick book, it was surprisingly light, he noted, turning to the one marked "Seven." Another of Melanie standing beside a very short Doctor dressed more conservatively, then more of him with a girl named Ace. Scratched out was the name Dorothy.

"Eight" was definitely taking after the Victorian style. There was one picture with him and two others, a woman and an Asian boy, labeled "Dr. Grace Holloway" and "Chang Lee" respectively.

More pictures, but Rory was getting a little tired and quickly paged to "Nine."

A very rough face looked up at him from the picture. As a nurse, Rory knew what people looked like when they came into the hospital, gravely wounded and the only survivor of whatever had befallen them. And this one had it in spades.

But the next page featured a young blonde girl, who couldn't be twenty. In delicate writing was "Rose Tyler." There were a lot of pictures, small, medium, large, on their own or sharing a page. The Doctor with Rose. Only one featured a Mickey Smith, but he had a look of jealousy on his face. Another man, this one labeled Captain Jack Harkness. Dressed in World War II clothing, Jack had a look of cockiness on his face as he winked at the camera.

He finally reached "Ten." This Doctor was, compared to his previous self, very happy, and wearing a brown pinstripe suit. More of himself and Rose. Another blonde woman in a picture with them, labeled Jackie Tyler. It was the first time a companion's parent was also present.

Stuck in the middle was a more recent picture of Sarah Jane Smith. She had obviously gotten older and one of the K-9 metal dogs was with her. In the same writing, he saw "My Sarah Jane. Until we meet again."

Abruptly, the pictures shifted to another young woman. Dark-skinned, Martha Jones grinned at the camera, but the Doctor, now in blue, was not smiling. Whatever had happened to Rose had caused him to regress mentally. Jack appeared again, with a note of Torchwood 3 attached.

Another man appeared, but he looked crazy. The caption read simply "The Master." Why the Doctor had a picture of him in the book, Rory didn't know, but was glad he'd never faced that guy.

The pictures shifted again. A redhead in a wedding dress, with a note that read, "After Rose, before Martha, after Martha." Not bothering to figure that one out, he browsed through more of the Donna Noble pictures. Some were splattered with heavy tears, others wrinkled from being held instead of preserved. Another picture, labeled "Sylvia Mott Noble and Wilfred Mott" showed Donna with her mother and grandfather. Underneath the names was written, "Donna Noble: The most important woman in the universe."

A young blonde girl, the picture slightly blurry, was tucked into the pictures. She was grinning, a forest in the background. Its caption read "My daughter Jenny, born and died on Messaline."

To Rory's surprise, a photo of River Song was included standing alongside this Doctor. The caption for it read, "I saved her, but didn't. Spoilers."

Suddenly, a group photo: Sarah Jane, Mickey, Jackie, Rose, the Doctor back in brown, Martha, Donna, and Jack. Also in the picture was a second Doctor, wearing the blue suit. They were all around the old TARDIS console room. The old ship must've taken the picture herself.

A few more random pictures of the Doctor with one-off people. Another with him and Wilfred.

Then: "Eleven."

Rory sighed as he realized he had finally caught up. He quickly flipped through pictures of Amy and himself, paused at the ones with only Amy and the Doctor, especially during that time he had been erased from time. A few River Song pictures were also mixed in here, including one of baby Melody. A picture of Mels, Amy, and Rory was also present, one that he realized still sat in Amy's room on Earth. That was the last picture.

With a frown, Rory put the book back on the shelf. How was it that those pictures still existed when everything else was so messed up?

A soft noise caught his attention.

"Doctor?"

Rory swallowed, figuring he'd better play along. "Yeah?" he called out.

Amy stepped into the room, her white nightgown bright in the dark. Rory felt both hearts leap. It felt so weird.

"I – I thought you were in bed. Sleeping."

She grinned slyly at him, then the bed. "Do I look like I've been sleeping?"

Rory started to tremble as Amy fumbled with the bowtie. This wasn't supposed to happen, he thought in the back of his mind as the braces slid off and buttons started coming undone. This was…totally…and…and…_completely_ inappropriate…

He gave up three seconds later.

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Amy found herself in an old console room. Its stark whiteness served as a calming effect on her frayed nerves. If the computer thought she'd enjoy this fantasy, the only thing she'd enjoy would be tearing it apart with her bare hands.

She cried for Rory. She cried for Melody, Mels, and River, the same person, but so different. She cried for her parents.

A gentle hum, rising and falling, tried to sooth her.

"Amelia?"

The Doctor kneeled down beside her. "Amelia? Are you ok?"

Amy sniffled, then wiped her eyes with her sleeve. "I don't know, Doctor. Honestly. Can I just go home for a bit?"

Again, the confused look as he settled next to each other, offering a handkerchief. "Amelia, I tried that when you were ten. Don't you remember? Your Aunt Sharon tried to have me arrested. Said I was a child abductor and did things to you. That was ten years ago."

"Can you take me to Earth then? Anywhere on Earth? Literally?"

The Doctor jumped to his feet. "I know just the place!"

He took out of there without a backwards glance.

Amy glanced at a mirror on the old console. Her face was pale and white, with the exception of blotchy red cheeks. She sniffed, wiped her nose with the handkerchief, stood up, and squared her shoulders.

"Right, then," she said. "Time to find a way out of this sick Wonderland."

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The Doctor followed Romana into the Gardens. The last time he had seen this place, it had been covered in burning Dalek ships. Now the grass was fresh and red, the flowers a multitude of hues.

"There's someone here who's been waiting for you," said Romana.

In the middle of the Garden was a bench. And on this bench was a very familiar person.

"Hello, Sweetie."

The Doctor's jaw dropped. River was adorned in the orange robes of the Prydonian chapter, but her robes had definitely been…altered to more of her clothing style. Without the Time Lord hat, her curls were everywhere. She raised an eyebrow at him. For a moment, he swore he saw her close and tuck away a certain TARDIS-themed book.

"Were you expecting someone else, my love?"

He swallowed.

"No, not at all."

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I remember on the episode "The Girl Who Waited," Rory made a mention of knowing the Doctor has two hearts. That was the first time, I believe, that either of them has made mention of knowing this fact. Correct me if I'm wrong, I won't mind, just make sure you can tell me where and when.

Something else you'll note is that Amy is horrified by what the Matrix system thought her fantasy would be. That horror is becoming reflected in the program. Rory is rather curious about his fantasy, whereas the Doctor is completely entranced.

I love writing Rory's POV. Of the three, he's my favorite. I'll miss them when they leave; Moff had better not kill them off for real this time. River is there too, but she's her own category. Matter of fact, I dressed like her for Halloween, using her Utah outfit. The casual wear, not the astronaut suit.

You know what to do!


	5. Chapter 5

I'm late and for that I apologize. Where I am, it is Christmas already. I will try to have the next chapter up before the Christmas special but I will be at my brother's for Christmas lunch and we traditionally stay the day over there. If I'm late again, I'm late again, but won't say any spoilers regarding _DW&W_.

Back to a short chapter again, but this one sets up some very important stuff. I can assure you, having previewed it, that the next chapter is twice as long.

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Chapter 5

_Blood. Screams. Cries. Repeated, grating shouts of "Exterminate!"_

_Burning, everything and everyone burning. _

_Including himself, burning bright gold…_

With a sudden jerk, Rory was jolted awake. Breathing heavily, hearts pumping, he simply laid there, Amy's red hair splashed across his pale chest. On the ceiling, stars danced and twinkled. Two stood out from the rest. The first was big and red. The second was smaller and blue. Gallifrey and Earth. The planet where the Doctor was from and the one the Doctor chose to belong to. The one that had been erased from the universe, and the one that would exist for millennia more.

The nightmares fading from his mind, Rory sighed. He felt caught. On the one hand, he was more than Rory now; he was Rory the Time Lord. On the other, he had spent nearly 2,000 years as a plastic man waiting for Amy and wasn't about to take the feel of real skin for granted.

But when he closed his eyes and let his mind wander, he saw so much. He didn't remember a lot of it, but it was still pretty cool. If he focused on someone in history, his mind provided the info on that person. Idly, he wondered who in history would be interesting to pop in on. He could visit any time, any planet, any where he liked.

Amy stirred, opening her eyes. "Hey."

"Hey," he replied.

She snuggled closer. "So, where are we heading now?"

Rory thought, letting the information flow through him. "The Eye of Orion is pretty calm this time of year. Maybe we can have a picnic lunch there."

"Sounds good."

She slipped out of the bed, throwing the nightgown back on as she did.

"See you in a few."

As Rory sat up, a sharp pain shot through his head.

"Ow!"

Amy poked her head back in. "You all right?"

"Yeah. F-fine." It was gone just as quickly as it had come. "Right behind you."

She shrugged and left. Rattled, he scrambled to dress and was promptly out of the room in just a few minutes.

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Quietly, Amy reentered the main console room. The Doctor was flicking switches and turning gears. She paused as he glanced up at the screen. It was displaying Rory's information again. She opened her mouth to ask the Doctor if they had landed yet when she heard him muttering and withdrew from sight.

"-thought I made _sure_ she wouldn't ever want to come back. Hah, _Rory_ _Williams_. What would you have done if you had lived for Amy to choose _you_, eh? Worked as a _nurse_, gotten _married_ to her, had a bunch of kids, and lived in _boring_ old Leadworth until you both died."

She heard him flipping a few switches.

"Well, I wouldn't have it. Checked you out before I came back. Good thing, too, made me make sure I wouldn't overshoot that trial run. And all I had to do to secure her was put the TARDIS in a street long enough for him to run into, then vanish. Poof."

She closed her eyes and covered her mouth in horror. The Doctor had…had basically _murdered_ Rory. Without her parents and without Rory, she would have no ties to Earth.

Carefully, she schooled her face into a neutral expression, then stepped back into the console room.

"So, have we landed yet?" Her voice was cheery, but a bit forced.

"Sure have, we're in London, England, early 2012. They're getting ready for the Olympics, so there will be quite a lot of excitement going on out there. Arrived way before the last time I was here, so no chance of running into myself."

He grinned at her. She managed to force out a smile, trying to ignore the sudden pounding in her head.

"Well, then, let's go!"

She took off. The Doctor hesitated, before wiping the screens and, this time, deleting the file.

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The Doctor decided that he was definitely living a better life here. He had Gallifrey, he had his people, and, best of all, he had River Song. No spoilers. The only problem was a slight headache he seemed to be developing. It was probably due to an overload of information, he decided.

He found here that he had had several children with River. They were mostly grown now, following different paths. Most were Time Lords, with their own titles. One had opted for a normal life, living in what was considered rural on Gallifrey. He had seen his granddaughter Susan sketching the plans for the latest TARDIS model.

"Whatever happened to the old Type-40s?" he wondered aloud.

Susan looked up at him from her work. "All of those were decommissioned and destroyed, Grandfather."

"What about…?" he trailed off, uncertain of how this timeline had unfolded.

"Oh, the one that took a shine to you when we sneaked in the lot and the guards caught us? I think that one was also destroyed."

His hearts panged at the thought of losing the Old Girl. But as he stared up at the night sky, hearing grandchildren and great-grandchildren play in the house, hearing River laugh, untainted by Kovarian and the Silence, he could not help but want to stay in this place.

Forever.

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And now the Doctor is locked into his fantasy. Who will escape first, Rory or Amy? Find out tomorrow!

And only 4 reviews? I'm a bit sad. I do read the reviews and find them to be encouraging and uplifting. I actually considered not posting this story here once, but seeing if it could be submitted to the BBC instead. If someone knows of a way an American can submit an idea to the Moff and crew, let me know, ok? Won't stop me from posting to the end, of that I can assure you.

Ta!


	6. Chapter 6

Things are starting to roll now. Please enjoy and a very Merry Christmas to all, home and abroad.

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Chapter 6

Rory fiddled with the sonic screwdriver, trying to unlock the cell door. Beside him, Amy was tapping her foot.

"Well?"

"Sonic is having a hard time with the lock," he muttered, trying another setting. Just how many settings did this thing come with? And how was he supposed to know that Amy's saying a particular color wasn't very flattering on the Queen of Kratos was an executable offense to the offender and accomplice?

There was a click as that setting worked.

"C'mon," he whispered, checking for guards. Apparently, they didn't expect their prisoners to be able to escape, because there wasn't a soul in sight.

They dashed through corridors, past frightened people and surprised royal guards. It was only by luck that they were able to make it to the TARDIS, who had moved herself nearby to the royal gardens. Just as Rory shut and locked the door behind them, there was a ton of pounding on the door. It remained unyielding.

Rory started pulling levers, pressing buttons, and generally doing all he could to avoid looking his wife in the eye. She didn't take too well to being ignored.

"I'm getting tired of this," she said.

"Of what?"

She gestured wildly. "Of running for my life, of getting shot at, and locked up, and…and…"

She flopped down in the seat. "Just…take me home, ok?"

With a sigh, he let his hands follow some kind of pattern. Within minutes, they were on a street very close to the Pond house. Amy grabbed a few things and made for the door.

"Amy?" he asked tentatively.

"What?" she snapped.

He sighed again, stuffing his hands in his pockets. "Well, am I supposed to just drop you off or am I allowed to say goodbye?"

Amy gave him a cold stare. "Whatever."

And she was out the door.

He groaned. "Amy!"

He darted out behind her. Catching sight of her about twenty feet away, he ran to catch up.

"Amy?" he said.

"Leave me alone!"

"Amy! What did I do?"

She swung around. She was furious and Rory mentally took a step back.

"What did you do? You crashed in my garden when I was seven, then took off and I didn't see you again until I was nineteen! I spent two years searching for you, finally finding you and you didn't even want me on board at first."

_Ouch_, thought Rory. This Amy clearly had a lot more mental issues and had latched onto him. Some part of him wondered if maybe the Rory of this universe looked like the Doctor. If there was even a Rory at all.

"_Are you even listening to me?_"

"Go home, Amy."

She stared at him. "What?"

This wasn't what he wanted, but he knew it was what was needed.

"Go home, Amy. Go to your mum and dad, or whoever it is you have waiting for you at home." Rory's voice was flat, heavy, resigned.

Amy stared at him, mouth opening and closing, before running off. This time, Rory did not pursue her, but chose instead to return to the TARDIS.

Once back in, Rory closed his eyes and thought. The more he thought, the harder his head pounded.

"Right," he said out loud. "This is a fantasy world and I want out. How do I get out?"

The phone on the console started ringing. Rory stared at it. It kept ringing. Tentatively, he picked up the receiver and put it to his ear.

"Hello?"

"This is the Matrix Prime Virtual Reality Help Line," said a calm, female, automated voice. "If you wish to continue your virtual fantasy, please say yes. If you wish to leave, please say no."

"No."

"Please state your name."

"Rory Williams."

There was a pause and some music.

"Rory Williams, you have decided to leave the Matrix Prime Virtual Reality System. If you accept this to be true, please say yes and you will be withdrawn from the System. If this is false, please say no and you will remain in the System."

Rory gave a longing look at the TARDIS doors, then at his reflection. This world wasn't right. It was time to go.

"Yes."

A brilliant white light.

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Amy took off into downtown London. She didn't care where she went, so long as it was somewhere the Doctor wasn't.

She finally collapsed near a ruined building. A burnt flyer advertised clothing half off at Henrik's blew past her feet.

"Excuse me, Miss?"

She peered up at the police officer. He was staring at her with concern.

"Are you all right?"

She stood up, a bit wobbly. "Yeah, I'm fine."

He smiled. "What's your name?"

"Amy. Amy Pond."

"Well, Amy, Amy Pond. Any reason you're hiding near an abandoned building?"

"Just…just had to get away."

"Ah," he winked knowingly. "Boyfriend troubles?"

She swallowed. "Sorta, yeah." She stared up at the building. "What happened here?"

The officer looked up at it. "Eh, there was an explosion some years ago. Took out the top floor and cracked other parts and made it structurally unsound. But no one will buy it to fix it. Think it's cursed, see?"

She didn't, but kept quiet about that.

"Amelia!"

"Oh, no," she muttered.

"There you are!" the Doctor beamed. "I thought you'd gotten yourself into trouble! Again!"

She managed a smile. "No, Doctor, that's you."

The officer was staring at the Doctor, a frown now on his face.

"Well, come along, then, Pond. We've got more to do than hang around old buildings."

"Now wait a minute here," interrupted the officer. "I recognize your face and I do believe it's wanted."

"Oh, really? Someone wants this face?" He poked at the chin. "Mind you, it looks nice on me but–"

The officer reached toward his bobby stick. "I'm arresting you, sir, on suspicion of kidnapping and child molestation."

The Doctor looked unperturbed. "So she filed those charges after all."

"Might want to add murder to that list too," said Amy, hands gripped tightly at her side.

"And just who did I supposedly kill?" the Doctor sarcastically said.

"Rory. Rory Williams, from Leadworth. Died when his car hit an object that suddenly appeared in the middle of the road. Bit convenient, huh?"

A dark look came over the Doctor's face, and, for a moment, Amy's heart froze. She saw what the other beings in their travels saw: the anger and the fury of the last of the Time Lords, barely contained within his frame.

"You heard me. In the TARDIS."

She didn't trust herself to speak, only nodded.

The officer chose that moment to strike. The Doctor staggered as the stick made contact with his jaw.

"Run, Amy!" urged the officer.

And so, Amy ran. All that time she had spent with the Doctor, she put to good use. She ran for a mile solid, finally ducking into a pizza place. She gulped air down, lungs heaving.

"I need to get out of here, whatever this place is. Do you hear me!" she shouted, getting the attention of several patrons. "I want out!"

A phone rang. She looked around, but no one was answering it. She finally saw it on the wall of the parlor.

"Aren't you gonna get that?" she asked an employee, who was staring at her.

Startled, he looked at the phone. "Why? It's not ringing."

Wide-eyed, she reached over and picked up the receiver.

"Hello?"

"This is the Matrix Prime Virtual Reality Help Line," said a calm, female, automated voice. "If you wish to continue your virtual fantasy, please say yes. If you wish to leave, please say no."

Amy smiled. So there was a safety in the program after all.

"No."

"Please state your name."

"Amy Pond."

There was a pause and some music.

"Amy Pond, you have decided to leave the Matrix Prime Virtual Reality System. If you accept this to be true, please say yes and you will be withdrawn from the System. If this is false, please say no and you will remain in the System."

A hand suddenly gripped her shoulder. Startled, she was forcibly turned to see the Doctor there. His lower lip was cracked and bleeding and one of his eyes was blackened.

"Hello again, Pond. Thought you'd sneak away, did you?"

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Rory gasped as the VR-pod opened. The smell of lubricants was a stark contrast to the world he had left. Yanking the temple leads off, he patted himself down, assuring himself that he was back in his own skin. A quick hand over his chest reassured him he had only one heart. He turned to the other VR-pods.

Amy's face was pinched with pain as she appeared to squirm away from someone or something. Not sure what to do, Rory fumbled with the miniature control panel. It refused to open her pod.

"Amy! Amy!" he shouted.

He banged on the cover, ignoring the spots on his hands.

"Amy! Whatever is happening in there isn't real!"

He bit his lip and thought. Quickly, he pressed one of the temple leads back on, then jerked the other out farther so that it could be put on the miniature control panel to Amy's pod.

"This is probably a really bad idea."

There was a sizzle, then white.

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Evil!Doctor is kinda fun to write, in a twisted way. Er, that was a pun. Anyway, we're officially more than halfway through the story. If you can spare a min to write a review, that would be a very nice Christmas gift. Thanks.

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The First Doctor: Here's a toast, a happy Christmas to all of us.

Steven: The same to you, Doctor, Sara.

The First Doctor: And incidentally, a happy Christmas to all of you at home!

–_The Daleks' Master Plan_, broadcast 13 Nov 1965 – 29 January 1966.


	7. Chapter 7

Saw _DW&W_ last night, definitely a good episode. I'll not say any spoilers here, but trust me, worth watching.

No Doctor this chapter, focusing on Rory and Amy. I hope I have made their characters' reactions believable.

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Chapter 7

Amy shrank away, dropping the receiver. The Doctor advanced on her menacingly.

"No," she whispered, then realized what she said.

"Thank you for using the Matrix Prime Virtual Reality System. When you are ready to withdraw, please restate your request."

Then a busy tone. The Doctor grinned.

"Looks like it's just you and me now," he whispered, playing with her hair. She closed her eyes and turned her head away.

"Hey."

Hope rushed back as she recognized the voice. "Rory."

The Doctor turned around to face him. "Well, well, who do we have here?" he said condescendingly. "Competition? You wish."

Rory glared at him, the full fury of the Last Centurion barely in check. The auras of the two caused chairs to scrape and feet to scamper.

"Rory, be careful," Amy cautioned. "He's not our Doctor."

Keeping the pseudo-Time Lord in sight, Rory moved into a fighting stance, one from a memory of his Roman life. The Doctor moved into a different stance, one that Rory recognized from his experience as Venusian Akido, but it was a sloppy stance.

With a snarl, the Doctor leapt at Rory, aiming for his neck. Gracefully, Rory stepped aside, letting the Doctor slam into a nearby table. The Doctor stumbled, but did not let up.

"Amy, get out of here," said Rory.

"What? I'm not leaving you!"

"Amy, please!" He ducked another punch.

She scoffed. "I am not leaving you here with – with that!"

As Rory bobbed and weaved, Amy looked around, trying to find anything that might give Rory an advantage. She ducked into the kitchen. She grinned as her eyes alighted upon the perfect item.

Back in the dining area, the Doctor threw Rory over the countertop, smashing the tip jar and causing the register to fall to the ground.

"Rory, Rory, _Rory_, why can't you die and stay dead?" he growled.

Rory grimaced as he stumbled to his feet. "I suppose Death has a restraining order against me."

The Doctor barked out a laugh. "Then I suppose I'm going to have to break that restraining order and put you where you belong."

But the Doctor had barely gotten two feet when a pizza oven paddle was slammed into the back of his head. His eyes widened at the impact, then he slumped to the ground and didn't move. Stunned, Amy dropped the paddle, then ran to Rory.

"Rory, I'm sorry, I'm sorry," she sobbed.

"Shh, what for?"

She hiccupped. "This fantasy world. It knew I had wanted to travel with the Doctor since I was little, but it took that to mean I didn't want be with you."

He stroked her hair, trying to calm her down.

"Hey." He brushed a tear away. "Let's get out of here, ok?"

She nodded.

The phone rang again.

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Rory gasped as he collapsed to the floor. Amy's VR-Pod opened, and she tumbled out. For a moment, the two simply lay there on the backs, catching their breath.

Finally, they sat up and caught sight of each other.

"Rory?"

"Amy?"

Rory's hair, once sandy brown, was now a shiny, polished shade of silver. Crows' feet and facial wrinkles were present, as were a few spots on his hands. Amy's hair, once crimson red, was now snow white. She too, had wrinkles on her face, with smaller crows' feet near her eyes.

They touched each other's faces, marveling at the differences.

"The Doctor," said Rory suddenly.

They scrambled to their feet. Inside his tube, the Doctor lay calmly, still sleeping. His hair was still brown, but with grey and white threading through. He did have a few wrinkles now. Whereas before, he had looked at most 30, the Doctor now looked to be in his mid-40s. And if the ever increasing amount of hairs turning colors was a good indicator, he was probably getting closer to 50 with every breath.

"Where's Benedict?" said Amy suddenly.

"Dunno, he wasn't here the first time I came round."

The doors chose that moment to slide open. They whipped around to see Benedict standing in the doorway, mouth agape.

"Rory? Amy?" he asked.

"You forgot to mention this might be part of the problem," said Rory, indicating their aged bodies.

Benedict's eyes widened. He honestly looked like he hadn't expected whatever the virus was to affect them like this.

"Look, we need to get the Doctor out," said Amy. "Rory came into my fantasy by using the wires from his pod to connect to mine, but we can't use our pods again, the wires are burnt."

Indeed, the two VR-pods were still smoking a bit from the cross-wiring job Rory had done.

Benedict scrambled to Doctor's VR-pod. He input multiple commands. Each time, the pod's computer rejected him.

"I can't shut down his pod," Benedict whispered, shocked. "I've been locked out of the controls."

Rory glanced at the Doctor. He was still aging slowly.

"We need to get back in," he insisted.

"There's no telling how much more your bodies can stand," said Benedict. "An hour, two tops."

"The Doctor doesn't have time for us to wait about and find a solution," snapped Amy, Scottish brogue loud.

Rory's mind was working in overdrive. The memories of his time in the machine were slipping away faster than sand in an hourglass. He concentrated, grasping onto a few concepts left over. Quickly, he began gathering random computer bits of the ruined machines. Amy stared at him.

"Rory, what are you doing?"

"Trying to figure out how to use some of the spare parts around here and turn them into a synchronized brain wave analyzer so we can find what frequency of subsonic activity is keeping the fantasy going in his head. Then we can use this and this, with a bit of that, to connect our brain waves to the Doctor's VR-pod. Shame he's got the sonic screwdriver in there with him, would have made assembly easier."

Rory looked up from his rapid delivery to find Amy and Benedict staring at him, the former in absolute confusion and shock, the latter in glee.

"Yes, yes, and don't forget you need to install an energy buffer in case of a critical overload," agreed Benedict. Rory noted that, and grabbed an extra bit from a parts bin.

"Rory, what exactly did you pick up in there?" asked Amy. "Cause I've only ever heard the Doctor talk like that and you sounded just like him."

Rory didn't answer, simply plugged the wires into the small computer he had made near scratch.

"Here, take this," interrupted Benedict. He held out a pair of watches. "They're set for 90 minutes, they'll let you know how much time has gone by in the real world compared to the virtual one. It'll tap into your brain waves and project onto your skin. It'll look like you're really wearing them."

"Thanks," said Amy, strapping hers to her wrist. Rory followed suit, then offered one of the temple leads to Amy.

"Are you sure this is gonna work?" she asked warily.

Rory sighed. "No. But it's the only chance we've got. And his too."

A white flash.

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You have no idea how close I was to having Rory shift into his centurion outfit for the fight scene. But I think this works out better.


	8. Chapter 8

Another chapter, but now we head to Gallifrey. I did some research on what kind of glasses Matt Smith wears. Use Google Images and you'll find the image I used. Er, first page of results, last row, last image, as of today. I hope I described them right. Well, at least you'll see what I meant. Shutting up, now.

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Chapter 8

Quietly, the Doctor closed the book he was reading, took off the dark, thin, slightly-rounded reading glasses, and placed them both on the night table. Beside him, River stirred at his small motions.

"Sweetie?"

Turning off the lamp, he smiled as he slid down under the covers. "It's ok, just putting the book down."

She rolled back over. The copper-tinted moon was a crescent outside the window, yielding just enough light to see her lithe frame, tucked under Gallifreyan-accented sheets. A soft breeze blew in the scent of flowers, blooming on the silver-leafed trees near the house. Closing his eyes, he breathed deeply in, holding it, relishing the familiar aroma.

A crash downstairs broke the moment. He sighed and swung out of the bed.

"What's wrong?"

"Probably one of the grandkids in the kitchen again," he said, grabbing a housecoat with swirly writing on it. "I'll tend to it."

He made his way out of the bedroom, past other rooms, the doors sealed firmly shut. Confused, he cautiously stepped into the kitchen.

There, standing there just as confused as he was, were two humanoids. Humans, probably, from their 21st century style clothing. One was a red-headed woman; the other, a sandy-haired man with a Roman profile. But how did two humans get into the Presidential home?

"Who are you?" he asked.

"Doctor?" asked the woman. "It's us. Amy? Rory?"

He shook his head. "I don't know you."

She reeled back as if he'd slapped her. "Yes, you do! We travel with you, in your TARDIS!" Her Scottish brogue was heavy with indignation.

"Doctor?" said the man quietly. "It's us. Mr. and Mrs. Pond? Rory the Roman? Cracks in time? Any of that ring a bell?"

He straightened up. "I am the Doctor, Lord President of Gallifrey. And you are in my home."

Two guards appeared from behind him, in the traditional garb of Time Lord soldiers. One saluted him.

"Take these two out of my sight. I don't know how they were brought to Gallifrey, but they will not be leaving."

"Get your hands off me!" snapped Amy, throwing one's hands off her. But the guard was stronger than her and pinned her arms behind her back. Beside her, Rory struggled, but was unable to break the iron grip the guard had on him.

He watched with uncaring eyes as they were dragged away.

In the shadows, River smiled.

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"What's wrong with him!" exploded Amy.

They had been put into a cell, a very technologically advanced cell with an energy barrier instead of bars. There wouldn't be any breaking out of this one. Even if they had the sonic with them, it would have been as useful as a real screwdriver. And according to the watches, they had 83 minutes left.

"He's still in the fantasy," said Rory, sitting on one of the rather comfy beds. At least they treated their prisoners with a little respect. "And he's so entranced by it that he's denying reality. He fully believes he is on Gallifrey, that he's Lord President, and that we are not his friends."

"But _why_?" she said, flopping down beside him.

"He destroyed his own people, Amy, this whole planet, his family, his friends, all the people he grew up with," he said sadly. "Rejecting this reality means that he has to accept that he's on his own, last of the Time Lords and all that."

"You know a lot about him, don't you?" she wondered.

He smiled a bit. "I took a course in psychology to be a nurse." He took a deep breath. "Plus, in my fantasy, I was him."

"What?"

"Apparently, the machine thought my fantasy would be me as him. It was so real, I actually feel time flowing around me. I could feel the TARDIS in my head."

"Were you in his clothing?"

He said nothing, but a blush crept up his neck.

"You were! You were in tweed and braces and had that stupid bowtie on, didn't you?" She began to laugh.

"Oh, ha-ha," he muttered. "I tell you how it felt to be inside his head, and you're laughing at what I was wearing."

Amy snickered. "Tell you what, when we get back to the TARDIS, I'll see if I can find where he keeps his spare outfits. I have _so_ got to see with my own eyes."

He really regretted telling her now as her grin turned rather sensual.

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He paced up and down in his office. The two intruders from last night were really bothering him. They had seemed genuinely concerned for him and shocked when he didn't reciprocate.

The doors opening made him stop his pacing.

"There you are!" said the Master. It was so hard to think of him as Koschei, why was that? "I heard about last night."

The Doctor chuckled lightly, playing with a snow globe (doubling as a paperweight) version of the Citadel. "I think the whole planet's heard by now. You are quite the gossiper, aren't you?" He peeked at the other Time Lord through the liquid.

The Master scowled at him, his face looking like a carnival mirror. "I've been talking to security, blame them. It was a rather large security breach. Two humans appear out of nowhere, into _your_ home, of all places, and you're _not_ worried?"

The Doctor put the snow globe back down on the desk. "Course I'm worried, but if I'm visibly worried, what would that do, hmm? Now relax, I've got things under control."

The Master grumbled, but didn't argue. On his way out, he gave Amy and Rory, accompanied by guards, a disapproving look before sweeping away.

"In here," one of the guards instructed. "And don't touch anything."

"Hey, just because I'm human, doesn't mean I'm stupid," said Amy.

The other guard snorted, shoving Rory behind Amy into the room.

The office was very formal. Bookshelves, loaded down with, what else, books, as well as other items of varying intricacy. Framed pictures of Time Lords were hung around in various spots. A merry fire crackled in the fireplace.

"Well."

In a fancy chair, behind an even fancier desk, sat the Doctor. He was dressed in orange robes, with swirls of alien writing on them. A nearby pedestal held an odd hat that presumably matched the ridiculous outfit.

"Well, what?" said Amy bluntly.

He laced his fingers on the desk. "For starters, who are you two? Then, how did you get past the transduction barriers onto Gallifrey?"

Warily, Amy sat down in one of the chairs. Not meant to be comfy, Rory noted, wincing as he sat down.

"We told you. I'm Amy, he's Rory. We're the Ponds. We're from 21st century Leadworth, on Earth. We travel with you in your TARDIS."

"Impossible, I've never travelled off-planet."

"Doctor, please listen." Amy was practically begging. "We've got 70 minutes until we're all dead. This isn't real, this planet, the people here, they aren't real."

"Of course they're real, what else would they be?"

"They'd be dead." Rory's voice was cold, factual. "There was a war here, against the Daleks. The only way the universe could survive was both species had to be destroyed."

"No," said the Doctor, shaking his head.

"You were the one that did it! When the Daleks came to Gallifrey and the Time Lords wanted to destroy creation to save themselves, you were the one that triggered the device that blew both Time Lords and Daleks out of existence!"

"NO!" the Doctor bellowed, slamming his hands on the desk. The loud bang brought the guards running.

"Lord President?"

"I'm…I'm fine," he muttered, rubbing his head. "I've just got a bit of a headache."

"That's your memories trying to fight their way out," said Amy. "The machine we're in, it tried to suppress our memories, but it couldn't, not all the way, because it was working so hard on you."

"Guards, take them."

"Doctor, you've got to listen!" Rory shouted, struggling with the guard. He thought quickly. "Your fingers, they're burned, aren't they?"

With a frown, the Doctor looked at his fingers. "I must've accidentally burned them on my tea cup earlier."

Frustrated, Rory tried another tactic. "Theta! Theta Sigma!"

The Doctor froze. "How do you know my old nickname?"

"Nickname?" asked Amy as the guard's grip held her firmly. "What, they name their kids after letters of the Greek alphabet?"

"I found your name on a book on board the TARDIS. It had loads of pictures, of what you looked like in your past lives, all the people you travelled with."

"I told you, I've never–"

"Susan, Ian, Barbara, Jamie, Victoria, Zoe, Liz, Jo, the Brigadier, Benton and Yates, Sarah Jane, Leela, Romana, K9–"

"Stop. Just stop." He was rubbing his temples, a grimace on his face. The guards began to fade away.

"Tegan, Nyssa, Turlough, Adric, Peri, Melanie, Ace, Grace, Chang–"

The Doctor looked closer to pulling out his own hair. "I'm warning you now, _stop_."

"Rose, Jackie, Mickey, Jack, Martha, Donna, Jenny, Wilf–"

"I said, _STOP_!" The pain was getting harder to bear. The guards finally faded away.

Amy caught on. "And what of us, Doctor? What about my daughter, Melody?"

"What of her?" he asked through gritted teeth.

"She grew up, took the name River Song so she wouldn't accidentally reveal herself too early to us."

"Impossible, River Song is a full Time Lord, here on Gallifrey." He slumped back into his chair.

"You know here?" asked Amy.

"Of course I do. River Song is my wife."

"You rang, Sweetie?"

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If things aren't complicated enough, River's here. Cause_ Doctor Who_ isn't _Doctor Who _unless there's some hesitation about what comes next.


	9. Chapter 9

And now the plot twists. Enjoy.

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Chapter 9

He was glad she had shown up when she had. His head was pounding and it was all he could do not to scream in pain.

"River?"

"I'm here, it's ok," she whispered reassuringly. She turned to Rory and Amy. "So, you're the two making all the fuss."

"River? How did you get in here?" asked Amy.

"In where?"

"In here," said Amy. "This…fantasy."

River threw her head back and laughed. "Ah, does it really matter?"

Rory shook his head. "Melody, you don't understand, this place isn't real, we need to get out, all of us."

At those words, he looked around, expecting to hear a phone ring or whatever was used around here to communicate. Nothing happened.

"Melody, Melody, who's Melody?" she mocked, her tone reminiscent of Berlin.

"You're my daughter," said Amy, shocked at the cold tone River used. "You were conceived in the TARDIS, on our wedding night. Exposure to the time vortex made you what you are. Why Kovarian took you from us."

River drew a finger down the side of the Doctor's face. He sighed, then lapsed into unconsciousness.

"There, now we can talk."

As River turned to face them, Amy gasped. Where her eyes would be was nothing but dark pools of swirling liquid.

"It was so easy to trick him into believing this place was real." The words coming out of her mouth were deep and dark. "I've been feeding off such low-energy minds for so long. When the three of you hooked in, I knew, I _knew_, it was time."

"Time for what?" asked Rory. He checked his time. 54 minutes. Why was time suddenly going so fast?

"Time to leave the machine, by drawing upon the life-force of a Time Lord. It took a little of that precious energy to create such complex fantasies for the two of you. But him? Simply show him his planet back, and he's all mine."

"And what happens when you're out?" asked Amy.

She laughed. "What do you think happens? With his life-force powering me, I'll escape this worthless planet and spread to far more interesting minds."

"No you won't, because we won't let you," said Amy. "And once we get the Doctor back, you'll wish you hadn't tricked him."

"And what are the two of you going to do? You're humans, stuck inside my machine." River, or whatever it was that had taken her form, smiled wickedly at them.

"Amy, our time, it's gone down to 30 minutes."

"It would be so easy to freeze you here, like I just did, until your time runs out. You wouldn't notice a thing. But I've got to get busy myself and every drop of energy counts at this point. So, ta!"

They blinked and she was gone. There was a groan from the Doctor.

"Amy? Rory?"

"Doctor!" shouted Amy.

"Not so loud, Pond," he weakly said. "I feel like I've downed four of Jack's specialty hypervodkas. And at my age, that's _not_ a good idea."

Rory chuckled. "Yeah, you're back."

"Where are we?" he asked, getting to his feet. He noticed his attire. "Oh."

"Funny, I never thought of orange as your color," said Amy dryly.

He sighed. "It's my chapter color. On Gallifrey, families were divided into chapters, each chapter represented by a different color." He motioned to his own outfit. "The Prydonian Chapter's color was orange. It was also the chapter with the most Time Lord renegades."

Rory carefully looked him over. "Doctor, do you remember anything that's been happening recently?"

"You mean, do I remember some kind of hold on my mind, making me think I was back on my home planet, and that I didn't know the two of you, let alone anyone I'd travelled with?"

"Ummm, basically, yeah."

"And that," said the Doctor with a low tone, "was the second mistake. The first being that they threatened my friends."

He started to stalk out of the room, but tripped on the hem of the robe instead. He was both glad and a bit embarrassed for the Ponds to catch his arms.

"Doctor, you might want to take those off," said Amy.

With a huff and a thought, the fancy robes disappeared, to be replaced by his customary style, albeit with the long green coat instead of the tweed. He adjusted the red bowtie fondly.

"I forgot how irritating those robes were."

They strode out together and into a sea of chaos.

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Gallifrey was being torn apart. The orange skies were filled with panicked cries. Above them, hundreds of Dalek ships were swooping down on the population. Amy and Rory could only watch in horror as the ships sent massive waves of energy that caused people's skeletons to light up, then fall down dead.

Ignoring the Doctor, Rory ran to the nearest fallen. She had been in the outermost portion of the beam and was still alive.

"Stay still, I'm a nurse."

She chuckled dryly. "I'm no nurse, but I know when a regeneration is imminent. For your own good, I suggest you retreat."

Remembering Berlin, Rory scrambled back to the Doctor and Amy, hidden behind an alcove, as the woman lit up with golden energy. A minute later, a new person scrambled to her feet and, still sizzling with energy, ran to help another who would probably not make it through regeneration, judging from the high amount of blood loss.

"What is this?" whispered Amy.

"This is the Time War. The entity must have pulled it out of my memories."

Another wave of energy passed dangerously close and the woman that had just regenerated cried out as both she and the other wounded were vaporized.

"That was the Dalek tactic. Pass through with a wave of extermination energy, kill a bunch of Time Lords, cause those that managed to live to regenerate. When that happens, the energy spike registers on their machines, lighting up the freshly regenerated like a beacon. Then it's simply a matter of a second wave, intensified."

"That's horrible!" argued Rory.

"That was the kind of war fought in the last days. That one tactic wiped out a quarter of the population in one week."

"Couldn't you avoid it? Get to safety?"

The Doctor shook his head. "The Time Lords had always relied on the quantum force field to not allow foreign ships in and the transduction barriers to prevent unauthorized teleportation. So, of course, the Daleks went after those first."

"That's suicide!" said Amy.

"Of course it is, but like the kamikazes of World War II Japan, the Daleks didn't care how many of themselves they killed, so long as the barriers came down. And they went down very quickly."

Rory checked his watch. "Doctor, we've got 15 minutes to get out of here."

"Yes, let's get out of here," he agreed.

There was a ring. Surprised, the Doctor dug through his pockets and found a cell phone. It might have been the one Martha gave him years ago, but he didn't care. He opened it quickly.

"Without that creature to block them, the safety protocols are kicked back into place, the one in control of the fantasy wants out, the computer has to provide a way out. Hello?"

"This is the Matrix Prime Virtual Reality Help Line," said a calm, female, automated voice. "If you wish to continue your virtual fantasy, please say yes. If you wish to leave, please say no."

"No."

"Please state your name."

"The Doctor."

There was a pause and a bit of music.

"The Doctor, you have decided to leave the Matrix Prime Virtual Reality System. If you accept this to be true, please say yes and you will be withdrawn from the System. If this is false, please say no and you will remain in the System."

"Yes, yes, and yes."

The brilliant white engulfed the three of them just as another wave of Dalek energy passed through the alcove they had been hiding in.

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Done and out. Back to the real world now.


	10. Chapter 10

I believe the term used to describe inflicted wounds, whether mental or physical, on the Doctor is called Doctor!Whump. In which case, I think that term definitely can apply to this story. I'm still keeping it K-plus, but if you think it needs to be raised to T because of this chapter, let me know.

Next to last chapter, people. I eagerly read every review, but if I reply, well, that would be spoilers. (_wink_) I am happy to have surprised you with the last chapter and I can only hope that this chapter also lives up to, or better yet, surpasses, your expectations as we draw to a close.

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Chapter 10

Billows of smoke poured out of the VR-Pod the Doctor had been in. A zap separated Rory and Amy from the other machine and they fell to the floor, exhausted. The Doctor stumbled out of his VR-pod, dazed and with a shock of white hair that would have rivaled Albert Einstein. He shook his head.

"Right, remind me to never _ever_ enter another virtual reality simulation so long as I live."

Both Ponds gave thumbs up from their position. With a groan, he pulled them to their feet. They took a moment to examine themselves. Amy and Rory were now into their mid 60s, while the Doctor was just a little behind.

"Great, three geriatrics to save the world," muttered Amy.

"Well, it could have been worse, we could have _not_ made it," said Rory optimistically. Then his face dropped. "Unless this is like the Dream Lord thing."

"No, Rory, I can assure you we're in reality now."

"And you know that how?"

The Doctor grimaced. "Because I think things are about to take a turn for the worse."

He leaned against the nearest wall, struggling to breathe, his face suddenly white.

"I think my right heart just quit."

Rory quickly moved to check the Time Lord's chest. Sure enough, he could feel the left heart beating frantically, but there wasn't any motion from the right.

"How do we jump start it?"

"I need…one of you…to pound me…on the front, then…the back." He was starting to see spots now. "It won't hurt too much."

Rory glanced at Amy, who nodded. He balled his hands together, then slammed them into the Doctor's front. Amy did the same to the back. With a shudder, the heart restarted. It was weak, but at least it was back up and running.

"We need to get out of here and find Benedict," said the Doctor, massaging the sore area. "Too many things aren't adding up."

As if on cue, the doors slipped open and Benedict strode in.

And he was pointing a gun directly at the Doctor.

"I'm sorry, Doctor, but she told me she'd kill me if I disrupted her plans."

"The parasite that's been living in the computer, you mean?"

He shook his head. "She doesn't live in the computer, she _is_ the computer. When we were creating the VR system, a computer virus got in and hid. As more and more people used it, the bigger it grew and the more sentient it got."

"And this is why you should always have a good anti-virus running at all times," the Doctor remarked to Amy and Rory. "So what has she promised you, then? Riches, eternal glory, a computer model named after you?"

With a shaking hand, Benedict unbuttoned his shirt. "I get to live forever with her."

Where a normal chest would have been was instead a horrifying jumble of machine parts and scarred skin.

"I was working on the computers one day, and a VR-pod malfunctioned. When I tried to run a diagnostic, it blew up on me. If it hadn't been for one of the Zharytes knowing some human anatomy, I would have died. Once I was fixed and integrated into the system, she was able to communicate with me."

"Speaking of the Zharytes, where are they? Haven't seen one since we were strapped in."

"They've been assisting her."

"What, all of them?"

"As many as weren't necessary to keep the VR-pod systems running."

Benedict began to back out of the room. "I'm sorry, Doctor, I have to go."

With a near silent whoosh, the doors closed. There was a hiss-snap as the door locked securely. In the blink of an eye, the Doctor was already scanning the lock system with the sonic screwdriver.

"The lock appears to be on some kind of rotating frequency module. If I can just find the right…ah ha!"

The doors slid open, and they ran into the hallway. Apparently, Benedict either didn't know or couldn't believe someone could open that door without his approval once they were locked in. A small shadow caught their eyes, and they darted left and down a hallway. Up ahead, they saw the shadow disappear into a room. They slipped in the room as quickly and quietly as possible.

And froze at the sight.

"Oh, my…Doctor, is that what I think it is?" asked Amy.

"If you're thinking that that looks like a VR-pod that's been redesigned to have a very complex life support system, capable of fully transferring a consciousness from a computer to a human body, then yeah, it's exactly what you think it is."

There were Zharytes darting around the machine in the large room. The small creatures looked exhausted from tending to the machine, but still they worked. Whatever the entity was, it must have terrified them into subordination.

"Quick! Over here!" hissed Rory from behind a stack of crates. The two ducked behind them just as Benedict bustled into the room. The small man was nervous, still in possession of the gun.

The three watched as he touched the cold machine and flinched. Then he whipped around on one of the Zharytes.

"Is it ready?" he asked.

The Zharyte chittered and nodded. The Doctor supposed that only the receptionist knew Standard English, though why it wasn't being translated by the TARDIS's circuits, he didn't understand. Perhaps the aging was beginning to affect the connection he had with the TARDIS.

"Good. Dismissed."

The creatures were more than happy to comply, withdrawing as quickly as possible. Soon, it was just Benedict, the Doctor, Amy, and Rory in the room. Carefully, the Doctor edged out of their hiding spot. It wasn't easy; his bones creaked in protest. He held his empty hands up, showing he was unarmed.

"Benedict, you don't have to do this."

Benedict jumped, dropping the gun. The Doctor made no move toward it, letting him pick it back up.

"I don't have any choice," he pleaded, pointing it back at him. "She's already taken over the mechanical parts of me. If I fail her, she can kill me right quick."

With the gun still aimed at the Doctor, Benedict slowly began to back up towards the altered VR-pod. Carefully, he settled himself in and pressed the buttons to close the lid, dropping the gun to the floor as he did so.

"Benedict, no!" The Doctor rushed forward, but it was too late.

In the tube, black mist began to seep in instead of the white. It curled around him, cradling him; Benedict smiled. The smile quickly turned to panic when the black smoke began shoving itself into his mouth and nostrils. He screamed, then fell silent.

Carefully, the Doctor backed away from the VR-pod. There was a hiss, then it opened. Benedict stepped out, but it wasn't Benedict anymore. Whatever had entered him, was now in full and absolute control of his body. The Benedict they had known was dead.

"Ah, now, that's much better." He cracked his neck one way, then the other. "Now what to do next? Ah, I know."

He walked right up to the Doctor and slapped him with the back of his hand. With a small cry, the Doctor fell to the floor in shock.

"The Doctor, feared by billions, known as the Oncoming Storm, reduced to an old geezer."

"Not the first time," the Doctor retorted, Rory hauling him back up. "I found a way out of it then, and I'll find a way out this time too."

Benedict laughed, the cruel dark laugh and voice that had come from the virtual River.

"The only way you'll get your youth back, relatively speaking, is if I die. And I don't think that'll be happening any time either."

With a wave, a wisp flew from his fingers. A Zharayte that had re-entered the room at that moment stiffed as the wisp was sucked into its mouth. Its eyes turned black, and it froze, waiting for commands.

"You see, a little tendril is all it takes to posses someone. That little tendril will multiply inside a body until it can't contain it anymore. Then they'll be released, to find more hosts. Of course, I'm not advanced yet to travel through space, so I'll simply have to take the nearest ship." Benedict frowned at the Zharayte and it walked off, rather clumsily. "And I'll have to figure out a way of making the wisps independent of myself."

The Doctor tried a different tactic, carefully choosing his next words. "You don't have to do this. I know a planet where there are no humans; it's just a giant library. You could live there, in those systems, and not ever be bored."

"Whoever said I was bored! I want to conquer the universe and the only way to do that is to first eliminate those would kill me for simply existing. Humans are notorious for their shoot-first-ask-questions-never policy. Earth would be a nice starting point. After I get rid of all the humans here, locked in the pods."

"But these are human beings! They have the right to live!"

"Life is wasted on the living," Benedict snarled in response.

"Funny, that," said the Doctor, raising hard green eyes to meet Benedict's swirling black. "Old foe said that to me once. And I'm the one still here."

"Not for long, Doctor, not for long. Even though you've been disconnected, your energy levels have plummeted. I estimate you have no more than an hour to live." Benedict grinned. "Your companions, on the other hand, have 15 minutes.

"So choose Doctor. Try to defeat me, they die. Leave me alone, I'll restore them to their youthful appearance."

The Doctor took a good look at Amy and Rory. Their facial skin was beginning to sag as they passed 70. Benedict, or whatever was possessing him, was right; they didn't have much time left.

He turned back round, only to find that Benedict had vanished.

"Where'd he go?"

"I think he just dissolved," said Rory, a bit loudly.

"Sorry, what?" shouted Amy.

"I said, I think he just dissolved!"

"You've been what?"

The Doctor sighed, then touched one pointer finger to each of their temples.

_Ponds, listen to me, you've lost your hearing. I'm going to keep a telepathic link open between the three of us. It won't be easy, but you should be able to push messages through so long as we stay within ten feet or so of each other._

He carefully withdrew his fingers, putting as much energy as he could into keeping the link open. They didn't know it, but he had put a bit of his mind in theirs. Nowhere near enough to burn them up, but it wouldn't be a good idea for them to keep it in their minds forever. It did, however, bring his time remaining to the same pace as them.

_Let's go_, he sent.

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It was hard trying to run when the three kept running out of breath. Rory and Amy had to stop twice. The Doctor tried to use his respiratory bypass system to push himself further, but found that that particular system wasn't working. His hears were pounding in his ears, and he felt every inch his millennium of years. There was nothing he wanted more than to sit down and close his eyes, to rest…

_Doctor!_

Amy's mental cry startled him back to reality. Rory had stumbled, and it was all Amy could do to keep her husband standing.

_My body's nervous system is starting to go out_, Rory thought. _Won't be long until the involuntary systems start shutting down. _

_No, don't talk like that_, snapped Amy before the Doctor could respond. _You are not dying on me again. _

Rory chuckled weakly, but wobbly remained standing.

_Come along, Ponds_.

They finally caught up with Benedict in the shuttle bay. He was typing on a keyboard, trying to override the controls to the large doors. Inside a nearby shuttle, the possessed Zharayte was starting up the craft. Carefully, the Doctor took out his sonic screwdriver.

"Benedict!" he called, holding it up. "Last chance!"

Benedict glared defiantly at the three. "I've already started the countdown that'll blow this planet apart! Do you really think I'd be stupid enough to stick around?"

With the final press of a button, the shuttlebay doors opened, whipping the air about, and Benedict dashed into the shuttle. Before the doors closed, the Doctor activated the sonic. Inside, Benedict laughed, and waved goodbye as the Zharayte closed the doors. Amy and Rory instinctively ducked as the shuttle's engines came online and he blasted out of the bay. The Doctor stayed still and silent as the doors closed and everything calmed down.

_Doctor, what did you do? _asked Amy.

_I locked the controls so that the shuttle will hone in on the next largest body in this system_, he replied grimly.

_But…that's the sun_, realized Rory. _That thing is on a collision course with the sun!_

_And he won't even realize it until he tries to turn away. By then, it'll be too late._

"Five minutes to planet-wide destruction."

The bay started to shake as the female voice calmly but loudly repeated this twice more. Klaxons washed the shuttle bay with a mauve tint.

_Um, Doctor? _said Amy. _Now what?_

The Doctor grinned. _Basically…run._

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This chapter was very long and very much littered with references from other episodes. Also, did anyone catch the name Benedict? On this side of the pond, Benedict was the first name of a certain traitor during the War for Independence. Or, if you are British, he was a hero. All depends on perspective.

Tomorrow, the epilogue. Still working, actually, on the bonus content. Having a hard time acquiring some information needed, but I can't ask y'all because that would spoil it.


	11. Chapter 11

I feel like I might have thrown in a bit of _dues ex machine_ into the story. But I did warn at the beginning it was a reference, so…I don't know. Either way, last chapter.

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Chapter 11

They darted out, looking every which way.

_Now, if I wanted to set a self-destruct switch, where would I put it? _mused the Doctor.

_I vote for his office,_ volunteered Rory.

_Excellent idea!_

Hearts pounding and adrenalin pushing them, the three bolted for Benedict's office. There, conveniently, was the machine, a large computer set into the wall, lights red and the countdown at 2:30. He whipped out the sonic, but the system was evidently protected from that sort of tampering. Instead, the Doctor began flipping switches, turning the lights from red to green. As the last of them changed color, the screen displayed a message.

_Enter passcode to terminate self-destruct._

"Ah. Well, that was an eventuality, I suppose. Don't reckon there's a password hint?"

Only 1:15 left. The Doctor was pacing as Amy and Rory collapsed into the nearby chairs. It was a tie between dying of old age or being blown up.

_Amy, in case we don't make it…_

_Shut up, stupid-head._

_In case we don't make it_, _I wouldn't have traded my time with you for anything._

She chuckled lightly. _Me either._

_20…19…18…_

"Think, think, _think_!

_17…16…15…_

The Doctor paused in his pacing. The answer had been staring at him the whole time. He rushed to the display and entered in _MORPHEUS._

"Self-destruct cancelled."

The countdown was frozen at 11 seconds.

The Doctor let out a loud "_HA_!" as the shaking ceased. He ran to the window just in time to see a small explosion as Benedict failed to override the controls. Whatever the entity was, it would be burned up quickly by the sun's corona as the debris was quickly engulfed.

He smiled as he felt the change wash over him, even from this distance. A whoop behind him told him that Amy and Rory's youth had also been restored.

"How did you know that was the right passcode?" asked Rory.

"Simple," he said, touching their temples and removing the mental link they'd had. "I watched the movie."

Amy's jaw dropped. "You guessed by putting in a random name from a _movie_?"

The Doctor grinned as he pointed at Benedict's desk. "Well, it looks like he watched the movie too."

There, on the desk, was a genuine, 21st century action figure of Morpheus from _The Matrix_.

"The Greek god of dreams as well," said the Doctor. "A fitting name, considering people entrusted their dreams to the Matrix when they chose to enter it." He wrinkled his nose. "Mind you, Morpheus could be a right grouch when he didn't get his beauty sleep. Worse than waking a _cat_, especially when his brother Phantasos, who did what you might call part-time work under him, decided to play practical jokes on him."

The Ponds just groaned as they followed the Doctor out of the room, who was still going on about Greek gods and their pranks.

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The TARDIS was still in the closet they had appeared in. A turn of the key later and they were safely inside. Immediately, the Doctor made for the controls, and they dematerialized. Something was still nagging at the back of Amy's mind, though.

"Doctor?"

"Yeah, Amy?"

"What you told Benedict, about a giant library? Can we go–?"

"_No_!"

She stared at him, eyes wide. "You don't have to shout, you know. We're not deaf. Well, not anymore."

His heartsbeat slowed back down. "We can't go to the Library."

"And…why not?" asked Rory.

He clenched and unclenched his jaw, focusing on a part of the console. "Because we can't." He bent his head. "It's…someplace I've been once, and…and I can't ever go back there."

How was he supposed to tell him he didn't want to desecrate their daughter's final resting place? A daughter that they had only just had, then lost, then seen her all grown up? He couldn't. He couldn't tell them the circumstances under which he had first met her. Not now, at least, if ever.

Rory could sense the burden associated with whatever had happened at this library. With a small tug on Amy's sleeve, they withdrew from the main console room.

The Doctor sighed as the central column gently rose and fell. In the back of his mind, the TARDIS tried to send reassuring emotions to him.

"Thanks, sexy," he murmured.

With a hum, the TARDIS gave a gentle nudge to the controls, sending them, not necessarily where they wanted to go, but where she knew they were needed. Now to see about finding Amy those spare clothes…

_THE END_

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I finally found the information I was looking for. Figures, all I had to do was admit that I couldn't find it and _Pop_!, there it was.

I hope that you enjoyed reading this story as much as I enjoyed writing it. There's still a matter of some bonus material that will be posted sometime tomorrow, then this story will be considered complete. No, there will not be a sequel. This was just the equivalent of a one-episode story.

As 2011 draws to a close, my hope is that 2012 proves to be even better.


	12. Alternate Endings

The following are alternate endings for this story. An extra treat, for those that decided to stick around till the end.

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_**Alternate Ending 1**_

"I can't stop it," said the Doctor. Everything he'd tried had failed. "I'm sorry."

He backed away from the machine as it counted down.

_11…10…9…_

Rory and Amy could only stare at him in disbelief.

_8…7…6…_

He turned his back on the machine and gave the two a final hug.

_5…4…3…_

"I'm sorry," he choked out.

_2…1…_

Everything turned white.

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The Doctor blinked as Benedict's worried face swam into view.

"Benedict?" he asked.

Benedict smiled. "There you are! We were beginning to think you'd never wake up!"

Behind him were Rory and Amy.

"Three days!" snapped Amy. "You were in that machine for three days! We were done in one day."

"Sorry?"

"At least we had the TARDIS to stay in," said Rory optimistically. "And the cooks here can whip up anything you ask for."

"So…the world didn't come to an end?"

Amy sighed. "Figures. Your fantasy _would_ be the same as your actual life."

She made for the TARDIS. Rory shrugged and followed.

Still confused, the Doctor bade Benedict goodbye ("Oh, please do come again!"), entered the TARDIS, and set the controls for their next destination.

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_**Alternate Ending 2**_

The Doctor happily jumped around the console, pulling levers, and throwing switches.

"So, where to now, Ponds?" he asked.

Amy shrugged. "Any chance we can go somewhere where vacation is not synonymous with running for our lives?"

"But running's fun!" argued the Doctor.

He looked up but the console room was empty.

"Amy?"

_Benedict smiled at the camera. "On Matrix Prime, you don't just live out your fantasies. Your fantasies become your life._"

"AMY?"

"I'm right here," she said, appearing from one of the upper rooms. "Rory had a question for me."

"Oh, okay."

"_Come today to Matrix Prime! We're running a special right now on long-term immersions."_

Adventures of all kinds, Rory and Amy running with him…

"_Imagine living in a world where you are always happy, always content, always taken care of."_

Sometimes River joined with them, sometimes Rory and Amy went off alone, and he and River had the whole TARDIS to themselves…

"_You owe it to yourself."_

They managed to fix the Library using a similar tactic that he had used at Lake Silencio, and River caught up with him afterwards. Both declared dead, they spent so many years after that on Earth. Amy and Rory had children (perfectly human children, no time-heads), and those children had children. Even the Doctor got his old job at UNIT back. Their decision to try for children was the best thing that ever happened to him. Even when his last regeneration died (Ginger! At last!), with River breathing her last beside him, some hundreds of years later, Earth, and the universe by extension, would be protected until the last star burned out.

_With a charming smile, the commercial ended._

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So, which ending was the real ending? Or are they all real?

The first alternate ending was simply that the whole story was a fantasy, taking place in the Doctor's mind and everything was fine in the end, no matter what happened. A perfectly innocent vacation.

The second alternate ending is reminiscent of the movie _Repo Men_, starring Jude Law. It was sort of the inspiration for this story in the first place. The parts in italics are paraphrased from the closing scene of the movie. It's a good movie, very rough, though, in terms of language, so I advise not letting children be in the same room when you do watch it. Basically, they hooked into the machine and never left. Kind of scary.

Thank you for reading and reviewing when you could.

Until next time.

~Jennifer R. Song


End file.
